Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F5 I175 R1	328	64.7	2582366	96.2%	2484236	120.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	449,442	A→G	V61A (GTC→GCC)	yajG ←	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	449,442	0	A	G	98.6%	248.7 / ‑3.8	71	V61A (GTC→GCC)	yajG	lipoprotein
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (32/38); total (32/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01

ATGATTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGACTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTG  >  NZ_CP009273/449307‑449577

atgatTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCtt                                                                                                                                      >  2:59885/1‑139 (MQ=255)

  gatTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCtttt                                                                                                                                    >  1:712382/1‑139 (MQ=255)

      tGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGcc                                                                                                                                 <  2:1193845/138‑1 (MQ=255)

      tGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGcc                                                                                                                                 <  1:1226047/138‑1 (MQ=255)

               aCCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGAt                                                                                                                       <  1:948855/139‑1 (MQ=255)

                 cGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCg                                                                                                                     <  1:848329/139‑1 (MQ=255)

                 cGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCg                                                                                                                     <  1:206222/139‑1 (MQ=255)

                   ggCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCgg                                                                                                                    >  2:1186062/1‑138 (MQ=255)

                    gCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTa                                                                                                                  <  2:881366/139‑1 (MQ=255)

                         tCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCt                                                                                                              >  1:344526/1‑138 (MQ=255)

                           ggACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGAt                                                                                                           <  1:36900/139‑1 (MQ=255)

                               caaccaTGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGc                                                                                                       <  1:146487/139‑1 (MQ=255)

                                 accaTGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCtt                                                                                                                                      <  2:564511/106‑1 (MQ=255)

                                 accaTGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCtt                                                                                                                                      >  1:564511/1‑106 (MQ=255)

                                 accaTGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCAc                                                                                                     >  2:1124093/1‑139 (MQ=255)

                                  ccaTGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGAt                                                                                                                       >  2:484833/1‑120 (MQ=255)

                                  ccaTGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGAt                                                                                                                       <  1:484833/120‑1 (MQ=255)

                                     tGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCAtt                                                                                                 <  1:59885/139‑1 (MQ=255)

                                     tGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCAtt                                                                                                 <  2:712382/139‑1 (MQ=255)

                                       tAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTaa                                                                                               >  2:977377/1‑139 (MQ=255)

                                       tAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTa                                                                                                <  1:1124093/138‑1 (MQ=255)

                                             cgcgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCg                                                                                                                     <  2:525378/111‑1 (MQ=255)

                                             cgcgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCg                                                                                                                     >  1:525378/1‑111 (MQ=255)

                                             cgcgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTa                                                                                         >  1:1014232/1‑139 (MQ=255)

                                             cgcgcgGTCATATGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGCTTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTa                                                                                         >  1:200745/1‑139 (MQ=255)

                                               cgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGTTTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACg                                                                                       >  2:133635/1‑139 (MQ=255)

                                               cgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCgg                                                                                                        <  2:284172/122‑1 (MQ=255)

                                               cgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCgg                                                                                                        >  1:284172/1‑122 (MQ=255)

                                               cgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACg                                                                                       >  1:275386/1‑139 (MQ=255)

                                               cgcgGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACg                                                                                       >  1:63899/1‑139 (MQ=255)

                                                           tttttCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGTTCGGCACCATTAATGCTTACGGTGACGCCCAt                                                                            <  1:1106923/138‑1 (MQ=255)

                                                           tttttCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCAt                                                                            <  1:817340/138‑1 (MQ=255)

                                                           tttttCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCAt                                                                            <  2:811733/138‑1 (MQ=255)

                                                           tttttCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATc                                                                           <  1:133635/139‑1 (MQ=255)

                                                           tttttCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGACTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCAt                                                                            <  2:1025733/138‑1 (MQ=255)

                                                                ccAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGc                                                                       <  2:1026085/138‑1 (MQ=255)

                                                                  aGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAAt                                                                                              >  2:275011/1‑113 (MQ=255)

                                                                  aGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAAt                                                                                              <  1:275011/113‑1 (MQ=255)

                                                                         cttGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCctg                                                             >  2:429403/1‑139 (MQ=255)

                                                                             cagcagGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCctgctg                                                          <  2:88674/138‑1 (MQ=255)

                                                                                   gAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAgt                                                   >  1:1092419/1‑139 (MQ=255)

                                                                                   gAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAgt                                                   >  1:300170/1‑139 (MQ=255)

                                                                                   gAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAgt                                                   >  1:1051468/1‑139 (MQ=255)

                                                                                   gAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATAGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAgt                                                   >  1:476650/1‑139 (MQ=255)

                                                                                      aCGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATAGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTa                                                <  2:476650/139‑1 (MQ=255)

                                                                                          aGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAAtcg                                            >  1:903562/1‑139 (MQ=255)

                                                                                                 gggAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGa                                     <  1:366544/139‑1 (MQ=255)

                                                                                                 gggAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGa                                     <  1:592898/139‑1 (MQ=255)

                                                                                                 gggAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTAGGATCCTGCTGTGGCAGTGTAATCGTCGGGGa                                     <  1:1108539/139‑1 (MQ=255)

                                                                                                  ggAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTaa                                               <  2:833449/128‑1 (MQ=255)

                                                                                                  ggAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTaa                                               >  1:833449/1‑128 (MQ=255)

                                                                                                      gCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCgg                                                                                                        <  1:254100/67‑1 (MQ=255)

                                                                                                      gCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCgg                                                                                                        >  2:254100/1‑67 (MQ=255)

                                                                                                         gTCAGGGGAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCaa                             >  1:581755/1‑139 (MQ=255)

                                                                                                              ggTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAgtt                        >  2:1238865/1‑139 (MQ=255)

                                                                                                                   cGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTgg                   >  2:91650/1‑139 (MQ=255)

                                                                                                                        tGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGAt                                                                 >  2:453107/1‑88 (MQ=255)

                                                                                                                        tGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGAt                                                                 <  1:453107/88‑1 (MQ=255)

                                                                                                                        tGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGtt              >  1:1093241/1‑139 (MQ=255)

                                                                                                                        tGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGtt              >  1:932886/1‑139 (MQ=255)

                                                                                                                        tGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGtt              >  1:673395/1‑139 (MQ=255)

                                                                                                                        tGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGt               <  2:1022536/138‑1 (MQ=255)

                                                                                                                               cgcgGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCa       >  1:212920/1‑139 (MQ=255)

                                                                                                                                gcgGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCa       <  2:788580/138‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  2:344526/139‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  2:212920/139‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  2:1023626/139‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  1:977377/139‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  1:867920/139‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  2:866661/139‑1 (MQ=255)

                                                                                                                                    gTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTg  <  1:749916/139‑1 (MQ=255)

ATGATTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGACTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTG  >  NZ_CP009273/449307‑449577

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 19 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TGGCTAACGATGATTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGACTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTGCAAGCATAAAC  >  NZ_CP009273/449298‑449588

TGGCTAACGATGATTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTG                                                                                                                                              >  SRR3722129.722844/1‑151 (MQ=60)

              TTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATC                                                                                                                                 <  SRR3722129.1243102/150‑1 (MQ=60)

                       aagagacagATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGA                                                                                                                       <  SRR3722129.491839/142‑1 (MQ=60)

                       AACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGA                                                                                                                       <  SRR3722129.962267/151‑1 (MQ=60)

                       AACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTG                                                                                                                        >  SRR3722129.349496/1‑150 (MQ=60)

                         CCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATC                                                                                                                     <  SRR3722129.860459/151‑1 (MQ=60)

                         CCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATC                                                                                                                     <  SRR3722129.209097/151‑1 (MQ=60)

                               CATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCctgtctcttatacacatctccg                                                                                                                >  SRR3722129.572883/1‑128 (MQ=60)

                                   CGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTA                                                                                                           <  SRR3722129.37355/151‑1 (MQ=60)

                                      cagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATG                                                                                                        <  SRR3722129.257686/89‑1 (MQ=60)

                                       CCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGC                                                                                                       <  SRR3722129.148530/151‑1 (MQ=60)

                                           CCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCctgtctcttatacacatc                                                                                                   >  SRR3722129.533052/1‑133 (MQ=60)

                                           CCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTAC                                                                                                   >  SRR3722129.1028552/1‑151 (MQ=60)

                                           CCATGTAACCACGCGCGGTCATATGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGCTTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTAC                                                                                                   >  SRR3722129.203553/1‑151 (MQ=60)

                                             ATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTgtctc                                                                                                 >  SRR3722129.288254/1‑146 (MQ=60)

                                             ATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGG                                                                                                 >  SRR3722129.279346/1‑151 (MQ=60)

                                             ATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGG                                                                                                 >  SRR3722129.64734/1‑151 (MQ=60)

                                             ATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGG                                                                                                 <  SRR3722129.60675/151‑1 (MQ=60)

                                               GTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGT                                                                                                <  SRR3722129.1139763/150‑1 (MQ=60)

                                                 gtgtataagagacagTCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGA                                                                                              <  SRR3722129.278969/135‑1 (MQ=60)

                                                                   GTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGTTCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGAT                                                                            <  SRR3722129.1122395/150‑1 (MQ=60)

                                                                   GTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATC                                                                           <  SRR3722129.135435/151‑1 (MQ=60)

                                                                   GTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGAT                                                                            <  SRR3722129.829085/150‑1 (MQ=60)

                                                                             cgccttagtctcgtgggctcggagatgtgtataagagacagGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGC                                                                 <  SRR3722129.459657/110‑1 (MQ=60)

                                                                                 TCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTG                                                             >  SRR3722129.1066227/1‑151 (MQ=60)

                                                                                 TCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTG                                                             >  SRR3722129.304458/1‑151 (MQ=60)

                                                                                 TCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTG                                                             >  SRR3722129.1107688/1‑151 (MQ=60)

                                                                                 TCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATAGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTG                                                             >  SRR3722129.483553/1‑151 (MQ=60)

                                                                                        GCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGT                                                      >  SRR3722129.916374/1‑151 (MQ=60)

                                                                                                CGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAC                                              >  SRR3722129.845426/1‑151 (MQ=60)

                                                                                                       CGCGGGAGGCGGTCAGGGGAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAAT                                       >  SRR3722129.590340/1‑151 (MQ=60)

                                                                                                         CGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAG                                     <  SRR3722129.601669/151‑1 (MQ=60)

                                                                                                         CGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAG                                     <  SRR3722129.371921/151‑1 (MQ=60)

                                                                                                         CGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTAGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAG                                     <  SRR3722129.1124025/151‑1 (MQ=60)

                                                                                                                      GGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTT                        >  SRR3722129.683343/1‑151 (MQ=60)

                                                                                                                      GGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTT                        >  SRR3722129.1108521/1‑151 (MQ=60)

                                                                                                                      GGGTAACGATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTT                        >  SRR3722129.946124/1‑151 (MQ=60)

                                                                                                                             GATTTGATTATCGCGGGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCAT                 >  SRR3722129.215884/1‑151 (MQ=60)

                                                                                                                                            GGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTGCAAGCATAAAC  <  SRR3722129.760863/151‑1 (MQ=60)

                                                                                                                                            GGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTGCAAGCATAAAC  <  SRR3722129.880313/151‑1 (MQ=60)

                                                                                                                                            GGTGGCTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTGCAAGCATAAAC  <  SRR3722129.991203/151‑1 (MQ=60)

TGGCTAACGATGATTTGCAGATTAACCGGGCCATTCGGACCAACCATGTAACCACGCGCGGTCATCTGTTTTTCCAGCACTTCTTGCAGCAGGAAACGCAGATCGCGGGAGGCGGTCAGGGTAACGATTTGATTATCGCGGGTGACTTTTGCCAGCGCCTGATCGGTACGCTGATCGGCACCATTAATGCTTACGGTGACGCCCATCAGGCTTGGATCCTGCTGTGGCAGTGTAATCGTCGGGGAAACTTCAATAGTTGTTGGCGGTTTTGCGCATCCTGCAAGCATAAAC  >  NZ_CP009273/449298‑449588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`