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 2,583,273 C→T 35.0% L68L (CTA→TTA) ‡ gadW → DNA‑binding transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,583,2730CT35.0% 87.6 / 64.9 114L68L (CTA→TTA) ‡gadWDNA‑binding transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (26/48);  new base T (9/31);  total (35/79)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.74e-01

Only 100 of 114 total aligned reads displayed.

CCGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCAGTCAC  >  minE/2583207‑2583327
                                                                  |                                                      
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:2950894/68‑1 (MQ=255)
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:1647067/68‑1 (MQ=255)
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:1003081/68‑1 (MQ=255)
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:1200908/68‑1 (MQ=255)
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:3170881/68‑1 (MQ=255)
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:1023857/68‑1 (MQ=255)
ccGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCt                                                       <  1:895557/68‑1 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTAc                                                     >  1:522933/1‑63 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:489739/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               <  1:42414/69‑1 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1852881/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1855374/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1997433/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:2281343/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:2366186/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:2477735/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               <  1:2519817/69‑1 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:2904200/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:2255862/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:3007590/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:60473/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:3123233/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:3252510/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1131471/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1072578/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1378476/1‑69 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               <  1:1024354/69‑1 (MQ=255)
       cgcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:138697/1‑69 (MQ=255)
        gcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCaa                                              >  1:866624/1‑69 (MQ=255)
        gcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCaa                                              >  1:584988/1‑69 (MQ=255)
        gcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCaa                                              >  1:1638381/1‑69 (MQ=255)
        gcgACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCa                                               >  1:1797541/1‑68 (MQ=255)
               cTGGATATCGAAGAGCTGAGAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1413155/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTatga                                       <  1:1699301/69‑4 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1224763/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1221059/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1011061/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:2593781/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:66838/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:2897359/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:710543/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:2945550/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1127931/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1125905/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:3017990/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1068111/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:3224348/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:552435/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1020961/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:2310360/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1518334/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1914824/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:2108150/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:2277193/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:753898/69‑2 (MQ=255)
               cTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1821443/69‑2 (MQ=255)
                    tatCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:2910683/67‑1 (MQ=255)
                    tatCGATGAGCTAACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:2943612/67‑1 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:2774271/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:2980762/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:3145222/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:3413571/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:2609820/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:393511/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGAttg                                    >  1:1171036/1‑66 (MQ=255)
                    tatCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCATCAGTTGCCACGCAATTTAGGAttg                                    >  1:141004/1‑66 (MQ=255)
                     atCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:1261081/66‑1 (MQ=255)
                            aGCTGACAGTTTGCCATTACTTACAAGATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAg                          <  1:894418/69‑1 (MQ=255)
                            aGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAg                          <  1:318750/69‑1 (MQ=255)
                            aGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAg                          <  1:1032317/69‑1 (MQ=255)
                            aGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAg                          <  1:2003529/69‑1 (MQ=255)
                              cTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAgga                                       <  1:1503421/54‑2 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:3341402/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:1566431/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:2514855/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:3422240/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:2812237/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:1657699/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:1066130/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTa                                    <  1:1926495/54‑1 (MQ=255)
                                 aCAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGt                     >  1:1297222/1‑69 (MQ=255)
                                      ttGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGtt                <  1:334465/69‑1 (MQ=255)
                                      ttGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGtt                <  1:376690/69‑1 (MQ=255)
                                      ttGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGtt                <  1:2525427/69‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:2446478/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:840428/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:851699/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:421648/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:3010231/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:239135/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:2204478/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:208992/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:1307065/68‑1 (MQ=255)
                                                ttacAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:1016615/68‑1 (MQ=255)
                                                  acAAAATATTCGTCAGCTACCACGCAATTTATGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:2684592/66‑1 (MQ=255)
                                                  acAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:474278/66‑1 (MQ=255)
                                                  acAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:2267206/66‑1 (MQ=255)
                                                  acAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:1432574/66‑1 (MQ=255)
                                                  acAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCa       <  1:947580/66‑1 (MQ=255)
                                                     aaaTATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCAGTCAc  <  1:3252562/68‑1 (MQ=255)
                                                                  |                                                      
CCGGATACGCGACGACTGGATATCGATGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGCTACCACGCAATTTAGGGTTACACAGCAAAGACCGTTTGTTAATTAACCAGTCAC  >  minE/2583207‑2583327

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