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 1,584,725 C→T 31.8% L69L (CTA→TTA)  cysZ → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,584,7250CT31.8% 63.1 / 33.6 72L69L (CTA→TTA) cysZpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (27/22);  new base T (18/5);  total (45/27)
Fisher's exact test for biased strand distribution p-value = 7.14e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

CATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCATCTCTGTGCTGTTAGTG  >  minE/1584657‑1584781
                                                                    |                                                        
cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                                          >  1:99375/1‑69 (MQ=255)
cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                                          >  1:2467445/1‑69 (MQ=255)
cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                                          >  1:2633070/1‑69 (MQ=255)
cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                                          >  1:2791060/1‑69 (MQ=255)
cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                                          >  1:3083086/1‑69 (MQ=255)
cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                                          >  1:3102091/1‑69 (MQ=255)
   tCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTAc                                                       <  1:1347821/69‑1 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:2060367/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:1258968/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:2155589/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:2349106/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:2465096/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:2608994/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:681218/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:2653982/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:276991/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:569570/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:3011016/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:1098697/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:3200632/1‑69 (MQ=255)
    cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                                      >  1:3250385/1‑69 (MQ=255)
          gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                                  >  1:2868340/1‑67 (MQ=255)
          gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                                  >  1:2500654/1‑67 (MQ=255)
          gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                                  >  1:500619/1‑67 (MQ=255)
          gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                                  >  1:3260482/1‑67 (MQ=255)
          gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                                  >  1:1060213/1‑67 (MQ=255)
             ctTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGa                                              >  1:1054691/1‑68 (MQ=255)
             ctTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGa                                              >  1:2495943/1‑68 (MQ=255)
                      acTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                                    <  1:1645628/68‑1 (MQ=255)
                      acTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                                    <  1:2552903/68‑1 (MQ=255)
                      acTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                                    <  1:2475477/68‑1 (MQ=255)
                       cTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                                    <  1:1631636/68‑1 (MQ=255)
                       cTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                                    <  1:476562/68‑1 (MQ=255)
                            tGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGc                               <  1:3013761/68‑1 (MQ=255)
                            tGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGc                               <  1:2895446/68‑1 (MQ=255)
                            tGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGc                               <  1:2876874/68‑1 (MQ=255)
                                tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg                          >  1:1512148/1‑69 (MQ=255)
                                tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg                          >  1:3186400/1‑69 (MQ=255)
                                tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg                          >  1:2313864/1‑69 (MQ=255)
                                tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg                          >  1:2309420/1‑69 (MQ=255)
                                tGGATCCCGACTCACATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCctct                           >  1:1599402/1‑68 (MQ=255)
                                  taTCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1823269/2‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgt                                     >  1:2885525/1‑56 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTgg                         >  1:1405565/1‑68 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTgg                         >  1:1656231/1‑68 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:2936995/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1030209/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:3093523/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1527644/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:3261801/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:509850/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:584755/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:2130018/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:2931278/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1645437/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:2290194/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1903735/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1912344/1‑69 (MQ=255)
                                  gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc                        >  1:1029222/1‑69 (MQ=255)
                                     cccGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGt                     >  1:1875702/1‑69 (MQ=255)
                                        gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:3258972/69‑1 (MQ=255)
                                        gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:2513585/69‑1 (MQ=255)
                                        gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:409736/69‑1 (MQ=255)
                                        gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:867232/69‑1 (MQ=255)
                                        gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:793840/69‑1 (MQ=255)
                                        gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:2332980/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:2472598/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:3245384/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:1731478/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:3400058/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:1180467/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:2721406/69‑1 (MQ=255)
                                         aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:3216630/68‑1 (MQ=255)
                                           tctcATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:1630439/66‑1 (MQ=255)
                                               aTGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc                 <  1:2346903/63‑1 (MQ=255)
                                                    ttACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCATCTCTGTGCTGtt      <  1:1365534/69‑1 (MQ=255)
                                                         ttCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCATCTCTGTGCTGTTAgtg  <  1:1910280/68‑1 (MQ=255)
                                                                  ggCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt                  <  1:2353068/43‑1 (MQ=255)
                                                                    |                                                        
CATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCATCTCTGTGCTGTTAGTG  >  minE/1584657‑1584781

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