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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,557,824 C→T 21.1% Q57Q (CAG→CAA)  bdm ← biofilm‑dependent modulation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,557,8240CT21.1% 153.8 / 34.7 71Q57Q (CAG→CAA) bdmbiofilm‑dependent modulation protein
Reads supporting (aligned to +/- strand):  ref base C (33/23);  new base T (7/8);  total (40/31)
Fisher's exact test for biased strand distribution p-value = 5.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.44e-01

AGGTTGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGT  >  W3110S.gb/1557755‑1557891
                                                                     |                                                                   
aGGTTGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGc                                                                     <  1:2671609/70‑1 (MQ=255)
    tGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTgg                                                                  >  1:3258143/1‑69 (MQ=255)
     gCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTa                                                                <  1:1910777/70‑1 (MQ=255)
           cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTg                                                                   >  1:1152783/1‑61 (MQ=255)
           cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:1852490/1‑71 (MQ=255)
           cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:1134231/1‑71 (MQ=255)
           cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:1156577/1‑71 (MQ=255)
              gCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      <  1:613526/71‑1 (MQ=255)
                   gCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGAt                                                 <  1:70496/71‑1 (MQ=255)
                   gCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGAt                                                 >  1:2309015/1‑71 (MQ=255)
                   gCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGAt                                                 >  1:2946861/1‑71 (MQ=255)
                    cACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGa                                                              <  1:1849611/57‑1 (MQ=255)
                    cACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCt                                                                    <  1:646278/51‑1 (MQ=255)
                    cACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCt                                                                    <  1:1071203/51‑1 (MQ=255)
                    cACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAgg                                                   >  1:226971/1‑68 (MQ=255)
                    cACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATg                                                >  1:1266235/1‑71 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:3430590/1‑51 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:2447825/1‑51 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:2303955/1‑51 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:1026100/1‑51 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           <  1:2098967/56‑1 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           <  1:3544294/56‑1 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGt                                            >  1:2664132/1‑71 (MQ=255)
                        ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGt                                            >  1:3501993/1‑71 (MQ=255)
                         tAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGt                                            >  1:4002580/1‑70 (MQ=255)
                                tAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGaa                                    <  1:3105924/71‑1 (MQ=255)
                                tAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGaa                                    <  1:267903/71‑1 (MQ=255)
                                  gggTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGc                                  >  1:3222930/1‑71 (MQ=255)
                                    gTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGa                                                              <  1:350139/41‑1 (MQ=255)
                                    gTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCtt                                >  1:270915/1‑71 (MQ=255)
                                    gTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCt                                 >  1:3694793/1‑70 (MQ=255)
                                          gCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAAcc                           >  1:3093575/1‑70 (MQ=255)
                                          gCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAAcc                           >  1:1651626/1‑70 (MQ=255)
                                            cACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGtt                                           <  1:153019/52‑1 (MQ=255)
                                            cACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGtt                                           <  1:1885152/52‑1 (MQ=255)
                                              cTGAGCACATAATTGAACGTTTGCTGTTAGATATCACTg                                                      <  1:1410884/39‑1 (MQ=37)
                                              cTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      <  1:3892334/39‑1 (MQ=255)
                                              cTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      <  1:2870684/39‑1 (MQ=255)
                                              cTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCAttt                      >  1:4073094/1‑71 (MQ=255)
                                              cTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCAttt                      >  1:1377729/1‑71 (MQ=255)
                                               ttaCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGt                                            <  1:1280003/46‑1 (MQ=255)
                                               tGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGt                                            <  1:2285068/48‑1 (MQ=255)
                                                gACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTgg                    >  1:2601714/1‑71 (MQ=255)
                                                gACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTgg                    >  1:2028667/1‑71 (MQ=255)
                                                gACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTg                     >  1:1751540/1‑70 (MQ=255)
                                                 aCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTg                     <  1:3674153/69‑1 (MQ=255)
                                                 aCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTg                     <  1:347270/69‑1 (MQ=255)
                                                 aCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTg                     <  1:2915985/69‑1 (MQ=255)
                                                 aCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTg                     <  1:1662326/69‑1 (MQ=255)
                                                 aCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTg                     <  1:2327487/69‑1 (MQ=255)
                                                     caTAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAAc                            >  1:1015834/1‑58 (MQ=255)
                                                     caTAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTc                  <  1:2572135/68‑1 (MQ=255)
                                                     caTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTAt                                         >  1:1382532/1‑45 (MQ=255)
                                                     caTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTAt                                         >  1:1103569/1‑45 (MQ=255)
                                                      aTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTc                                              <  1:1823325/39‑1 (MQ=255)
                                                      aTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTc                                              <  1:2733948/39‑1 (MQ=255)
                                                      aTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTc                                              <  1:3370905/39‑1 (MQ=255)
                                                      aTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGt                                            >  1:3996295/1‑41 (MQ=255)
                                                      aTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGt                   >  1:736539/1‑66 (MQ=255)
                                                        aaTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc             >  1:1980015/1‑70 (MQ=255)
                                                        aaTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc             >  1:475100/1‑70 (MQ=255)
                                                         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAg                                      >  1:2298625/1‑44 (MQ=255)
                                                         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAg                                      >  1:2428456/1‑44 (MQ=255)
                                                         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAg                                      >  1:3417894/1‑44 (MQ=255)
                                                            gATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCAt          >  1:2166541/1‑69 (MQ=255)
                                                            gATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTACAt          >  1:1605527/1‑69 (MQ=255)
                                                            gATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCAt          >  1:641883/1‑69 (MQ=255)
                                                             aTCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       <  1:3863198/71‑1 (MQ=255)
                                                             aTCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       <  1:1150873/71‑1 (MQ=255)
                                                             aTCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       <  1:2825237/71‑1 (MQ=255)
                                                             aTCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       <  1:1452767/71‑1 (MQ=255)
                                                                   tGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGt  >  1:225526/1‑70 (MQ=255)
                                                                     |                                                                   
AGGTTGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGT  >  W3110S.gb/1557755‑1557891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A