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 F1 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	478,533	C→T	A29T (GCC→ACC)	ylaB ←	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	478,533	0	C	T	98.3%	186.1 / ‑4.0	59	A29T (GCC→ACC)	ylaB	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (27/31); minor base A (0/1); total (27/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

AGCGCCTTGCCATCTTTCCAGCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAGGGAAAGTATAT  >  NC_000913/478402‑478655

aGCGCCTTGCCATCTTTGCAGCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGtcagccag                                                                                                                     <  1:841499/139‑1 (MQ=255)

        gCCATCTTTCCAGCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTaa                                                                                                             >  1:196762/1‑139 (MQ=255)

             cTTTCCAGCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGa                                                                                                        <  1:230571/139‑1 (MQ=255)

               ttCCAGCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACa                                                                                                      <  1:456018/139‑1 (MQ=255)

                    gCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGgcag                                                                                                 <  2:196762/139‑1 (MQ=255)

                                 aTCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa                                                                                    <  2:487016/139‑1 (MQ=255)

                                       cccTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGACAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGt                                                                              <  2:300252/139‑1 (MQ=255)

                                           tgtgTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCTGTACTc                                                                          >  1:746443/1‑139 (MQ=255)

                                           tgtgTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTc                                                                          >  1:583885/1‑139 (MQ=255)

                                            gtgtCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTcc                                                                         <  2:583885/139‑1 (MQ=255)

                                             tgtCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGgcag                                                                                                 <  1:773793/114‑1 (MQ=255)

                                             tgtCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGgcag                                                                                                 >  2:773793/1‑114 (MQ=255)

                                              gtCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCg                                                                       >  2:719355/1‑139 (MQ=255)

                                                                cGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGaaa                                                                    >  1:406816/1‑124 (MQ=255)

                                                                cGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGaaa                                                                    <  2:406816/124‑1 (MQ=255)

                                                                cGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGAt                                                     >  2:309382/1‑139 (MQ=255)

                                                                 gAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATg                                                    >  1:528086/1‑139 (MQ=255)

                                                                  aaTAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTa                                                                             >  1:323122/1‑113 (MQ=255)

                                                                  aaTAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTa                                                                             <  2:323122/113‑1 (MQ=255)

                                                                         aCGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCg                                                                                                         <  1:647436/78‑1 (MQ=255)

                                                                         aCGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCg                                                                                                         >  2:647436/1‑78 (MQ=255)

                                                                            cgGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCa                                         >  2:297724/1‑139 (MQ=255)

                                                                                      aGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATc                               <  1:309382/139‑1 (MQ=255)

                                                                                         tATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCtt                            >  2:410657/1‑139 (MQ=255)

                                                                                            ccAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCttatt                         >  1:271877/1‑139 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGa                                                                                                                    >  2:323521/1‑47 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGa                                                                                                                    <  1:323521/47‑1 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTc                                                  >  1:161008/1‑113 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTc                                                  <  2:161008/113‑1 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCAc                                        <  2:98919/123‑1 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCAc                                        >  1:98919/1‑123 (MQ=255)

                                                                                             cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCttatta                        >  1:666813/1‑139 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCTGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  2:746443/139‑1 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  1:719355/139‑1 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  2:666813/139‑1 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     >  1:234918/1‑139 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  1:484942/139‑1 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  1:47168/139‑1 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  1:274867/139‑1 (MQ=255)

                                                                                                ctctTCAATAAACGATGTTTCTACCTGCTGATGGATCAGCCAGATGCGTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACACCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  1:106679/139‑1 (MQ=255)

                                                                                                 tctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAacac                    <  2:271877/139‑1 (MQ=255)

                                                                                                 tctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAacac                    <  2:528086/139‑1 (MQ=255)

                                                                                                  ctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCaa                                                                                              >  2:347789/1‑64 (MQ=255)

                                                                                                  ctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCaa                                                                                              <  1:347789/64‑1 (MQ=255)

                                                                                                  ctTCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAAcaca                   >  2:371911/1‑139 (MQ=255)

                                                                                                   ttCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     >  1:806398/1‑136 (MQ=255)

                                                                                                   ttCAATAAACGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  2:806398/136‑1 (MQ=255)

                                                                                                         aaaCGATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAgg            <  2:234918/139‑1 (MQ=255)

                                                                                                             gATGTTTCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAGGGaaa        >  1:166099/1‑139 (MQ=255)

                                                                                                                   tCTACCTGCTGATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAGGGAAAGTatat  <  1:215219/139‑1 (MQ=255)

                                                                                                                         tgctgATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGa                                                                                        <  2:554329/47‑1 (MQ=255)

                                                                                                                         tgctgATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGa                                                                                        >  1:554329/1‑47 (MQ=255)

                                                                                                                           ctgATGGGTCAGCCAGATGCTTAAGCCGACAGgcag                                                                                                 <  2:662465/36‑1 (MQ=255)

                                                                                                                           ctgATGGGTCAGCCAGATGCTTAAGCCGACAGgcag                                                                                                 >  1:662465/1‑36 (MQ=255)

                                                                                                                           ctgATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     <  2:577218/112‑1 (MQ=255)

                                                                                                                           ctgATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAaca                     >  1:577218/1‑112 (MQ=255)

                                                                                                                           ctgATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAGGGaaa        >  2:91777/1‑125 (MQ=255)

                                                                                                                           ctgATGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAGGGaaa        <  1:91777/125‑1 (MQ=255)

                                                                                                                              aTGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAg                                                                               <  2:433942/51‑1 (MQ=255)

                                                                                                                              aTGGGTCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAg                                                                               >  1:433942/1‑51 (MQ=255)

AGCGCCTTGCCATCTTTCCAGCTCCTGCAGCGCATCTTTCCCTTGTGTCGCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGAATCAGTACTCCCGAAATAAGGCCGACCAGATGTCGTGTTCTCACCAGCATATCCTTATTAACACAGTGTAGGGAAAGTATAT  >  NC_000913/478402‑478655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A