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 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,697,000 T→C 24.3% intergenic (+69/‑49) suhB → / → yfhR inositol monophosphatase/predicted peptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,697,0000TC24.3% 99.9 / 27.1 82intergenic (+69/‑49)suhB/yfhRinositol monophosphatase/predicted peptidase
Reads supporting (aligned to +/- strand):  ref base T (51/11);  new base C (2/18);  total (53/29)
Fisher's exact test for biased strand distribution p-value = 7.85e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGGATGATAAAGAAGTCGCA  >  minE/1696941‑1697065
                                                           |                                                                 
cGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActt                                                          <  1:2223107/69‑1 (MQ=255)
cGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActt                                                          <  1:1803772/69‑1 (MQ=255)
cGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActt                                                          <  1:2695633/69‑1 (MQ=255)
cGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActt                                                          <  1:1719741/69‑1 (MQ=255)
cGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActt                                                          <  1:1430800/69‑1 (MQ=255)
 gggTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActt                                                          <  1:2448408/68‑1 (MQ=255)
 gggTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACCGCTTTActtt                                                         >  1:1971720/1‑69 (MQ=255)
 gggTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACCGCTTTActtt                                                         >  1:610091/1‑69 (MQ=255)
      atatCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTActttcttt                                                     >  1:210566/1‑68 (MQ=255)
           actcacCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCAc                                               >  1:2881321/1‑69 (MQ=255)
                        cGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCccac                                       >  1:433648/1‑64 (MQ=255)
                        cGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCt                                  >  1:1876239/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:764381/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:520659/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:1651154/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:2673568/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:3270538/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:1085860/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:2889323/1‑69 (MQ=255)
                           cTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTc                               >  1:287214/1‑69 (MQ=255)
                                  gcgcTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGAtt                        <  1:2632326/69‑1 (MQ=255)
                                  gcgcTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGAtt                        <  1:1167751/69‑1 (MQ=255)
                                  gcgcTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGAtt                        <  1:135250/69‑1 (MQ=255)
                                  gcgcTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGAtt                        <  1:1463894/69‑1 (MQ=255)
                                  gcgcTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGAtt                        <  1:1660145/69‑1 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCActct                                            >  1:1803398/1‑41 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:239180/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:2471105/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:2677562/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:2947331/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:380794/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:3114826/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:3234106/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:3369562/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:909604/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:1857111/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:1228546/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:678565/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:1674782/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:1352218/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:70712/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:1099123/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:931618/1‑43 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:324382/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:1128737/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:2958457/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:1038741/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:555368/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:1018428/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:3307158/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:3309525/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:3406489/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:2700161/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:1479/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:790806/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:156393/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:3409139/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:160532/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:2469760/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGgat                 >  1:2170961/1‑68 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTGCCCGATTAATgg                   <  1:2245017/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:573220/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:942260/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:1760555/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:1035072/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:1174729/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:1551639/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:1601003/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:166203/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:3382428/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:176223/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:1794021/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:2102672/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:2222977/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:2242322/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:2534088/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:2549115/66‑1 (MQ=255)
                                          ccGAAATACTTCCTCACCGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATgg                   <  1:3330154/66‑1 (MQ=255)
                                          ccGAAATACTTACTCACTGCTTTACTTTCTTTCGTCACTCTcc                                          >  1:702700/1‑43 (MQ=255)
                                                     ccTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGGATGATAaagaag       >  1:681604/1‑67 (MQ=255)
                                                     ccTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGGATGATAAAGAAGt      >  1:1079835/1‑68 (MQ=255)
                                                        cACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGGATGATAAAGAAGTCGCa  >  1:860191/1‑69 (MQ=255)
                                                           |                                                                 
CGGGTGATATCACTCACCCGCCCTCGCCTTTCAGGCGCTATTCCGAAATACTTCCTCACTGCTTTACTTTCTTTCGTCACTCTCCCACCATCTTTCCCCGATTAATGGATGATAAAGAAGTCGCA  >  minE/1696941‑1697065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A