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
A3 F28 I1 R1	161	50.8	1735388	98.6%	1711092	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,047,286	C→T	L220L (CTG→CTA)	gfcD ←	putative lipoprotein GfcD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,047,286	0	C	T	95.6%	141.8 / ‑1.7	45	L220L (CTG→CTA)	gfcD	putative lipoprotein GfcD
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (21/22); total (22/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01

TTACCGCGTTCATAACTCAGGTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTCAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGATGACAATATTTATCGCTCACCCG  >  NC_000913/1047152‑1047420

ttACCGCGTTCATAACTCAGGTTGATATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGCTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACg                                                                                                                                   <  2:285920/140‑1 (MQ=255)

      cgTTCATAACTCAGGTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAgggg                                                                                                                             >  1:416147/1‑140 (MQ=255)

        ttCATAACTCAGGTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGAt                                                                                                                           >  1:234585/1‑140 (MQ=255)

            tAACTCAGGTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCa                                                                                                                       <  1:280402/140‑1 (MQ=255)

                tCAGGTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGc                                                                                                                   <  1:337762/140‑1 (MQ=255)

                   ggTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGtt                                                                                                                <  1:722838/140‑1 (MQ=255)

                    gTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGttt                                                                                                               >  1:386175/1‑140 (MQ=255)

                    gTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGttt                                                                                                               >  1:240643/1‑140 (MQ=255)

                       gagaTCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGAt                                                                                                            >  1:256100/1‑140 (MQ=255)

                          aTCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACt                                                                                                         >  2:782318/1‑140 (MQ=255)

                            cTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTCAGACGCAGGGGATTCCACGGCGTTTGATACTCa                                                                                                       >  2:343430/1‑140 (MQ=255)

                              gCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGc                                                                                                                   <  1:550324/126‑1 (MQ=255)

                              gCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGc                                                                                                                   >  2:550324/1‑126 (MQ=255)

                              gCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTg                                                                                                              <  1:190111/131‑1 (MQ=255)

                              gCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTg                                                                                                              >  2:190111/1‑131 (MQ=255)

                              gCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAAt                                                                                                     <  2:240643/140‑1 (MQ=255)

                                 cAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATgcc                                                                                                  <  1:584183/140‑1 (MQ=255)

                                  aGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATgccg                                                                                                 >  2:423841/1‑140 (MQ=255)

                                  aGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATgccg                                                                                                 >  2:686731/1‑140 (MQ=255)

                                   gCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATgccgc                                                                                                <  1:816378/140‑1 (MQ=255)

                                    cTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATgccgcc                                                                                               >  1:753256/1‑140 (MQ=255)

                                     tGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCa                                                                                              <  2:721157/140‑1 (MQ=255)

                                         aGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATAGTCAATgcc                                                                                                  >  2:777022/1‑132 (MQ=255)

                                         aGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATgcc                                                                                                  <  1:777022/132‑1 (MQ=255)

                                               aTAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAg                                                                                    >  1:301460/1‑140 (MQ=255)

                                                        gcCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGc                                                                                   <  1:597035/132‑1 (MQ=255)

                                                        gacGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGc                                                                                   >  2:597035/3‑132 (MQ=255)

                                                         ccGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACg                                                                          <  2:234585/140‑1 (MQ=255)

                                                                     tGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCt                                                              <  2:416147/140‑1 (MQ=255)

                                                                        cTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTaaa                                                           >  2:380682/1‑140 (MQ=255)

                                                                         ttGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAg                                                          <  1:686731/140‑1 (MQ=255)

                                                                          tGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGc                                                         <  2:753256/140‑1 (MQ=255)

                                                                            ccTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTg                                                       >  1:795611/1‑140 (MQ=255)

                                                                              tGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGat                                                     <  1:423841/140‑1 (MQ=255)

                                                                                    aGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGcc                                               <  2:795611/140‑1 (MQ=255)

                                                                                      tttGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCg                                             >  2:111390/1‑140 (MQ=255)

                                                                                                  aTCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGAct                                 <  1:111390/140‑1 (MQ=255)

                                                                                                       tCTGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCACCGTGAGACTCTgcg                            >  1:152351/1‑140 (MQ=255)

                                                                                                         tGGTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGcgcg                          <  2:301460/140‑1 (MQ=255)

                                                                                                           gTAATTGTTTCCATCGTATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGAt                        >  1:205794/1‑140 (MQ=255)

                                                                                                                           tATTCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGATGACAATATTTATCGCt        <  2:262988/140‑1 (MQ=255)

                                                                                                                             ttCGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGATGACAATATTTATCGCTCa      >  2:109540/1‑140 (MQ=255)

                                                                                                                               cGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGATGACAATATTTATCGCt        >  2:14506/1‑136 (MQ=255)

                                                                                                                               cGAGTTTTAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGATGACAATATTTATCGCt        <  1:14506/136‑1 (MQ=255)

                                                                                                                               cGAGTTTCAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCG‑‑TCGTGAGACTCTGCGCGATGACAATATTTATCGCTCACCCg  <  1:343430/140‑1 (MQ=255)

TTACCGCGTTCATAACTCAGGTTGAGATCTGCCCAGCTGGCAGCGCGATAAACTGCGCCGACGTTGAAATGGCTTGCCTGAGGCAGTTTGCCAGCGAAATCATTCTGGTAATTGTTTCCATCGTATTCGAGTTTCAGACGCAGGGGATTCCACGGCGTTTGATACTCAATGCCGCCAAAGATGGAAGCCGGGCCACGAAAGATATCGCTAAAGCTGATATCGCCCGCATCGTGAGACTCTGCGCGATGACAATATTTATCGCTCACCCG  >  NC_000913/1047152‑1047420

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A