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 426,121 T→C 30.0% K264K (AAA→AAG)  nagB ← glucosamine‑6‑phosphate deaminase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE426,1210TC30.0% 75.9 / 38.3 83K264K (AAA→AAG) nagBglucosamine‑6‑phosphate deaminase
Reads supporting (aligned to +/- strand):  ref base T (34/24);  new base C (12/13);  total (46/37)
Fisher's exact test for biased strand distribution p-value = 4.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGACCCCCGATTTTAAAAAATATTGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCATGGTGGAAGG  >  minE/426054‑426189
                                                                   |                                                                    
cTGACCCCCGATTTTAAAAAATATTGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCt                                                                      >  1:2235521/1‑68 (MQ=255)
cTGACCCCCGATTTTAAAAAATATTGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCt                                                                      >  1:817246/1‑68 (MQ=255)
                     taatGCCCTGAGCAATGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:717603/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:1845473/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:3294064/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:2869375/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:2042772/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:639475/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:2164029/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:826174/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:1391531/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:1387165/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:956594/4‑69 (MQ=255)
                     taatGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCCTTGATATTTTCTGCTTCTAAtt                                                >  1:2259754/4‑69 (MQ=255)
                              gAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAat                                       <  1:2180533/69‑1 (MQ=255)
                              gAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAat                                       <  1:2078077/69‑1 (MQ=255)
                              gAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAat                                       <  1:3344656/69‑1 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTc                   >  1:2887715/1‑68 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTc                   >  1:1161887/1‑68 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTc                   >  1:3052414/1‑68 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTc                   >  1:3363071/1‑68 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:3249708/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:3324189/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:2728386/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:2676427/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:2530210/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:396082/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:535276/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:2415419/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:673666/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:885331/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:92068/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:98098/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:1623583/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:2086329/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:122584/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCa                  >  1:1988660/1‑69 (MQ=255)
                                                   aTAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTATTAACTTTCa                  >  1:2704217/1‑69 (MQ=255)
                                                      aCAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGc                >  1:1616997/1‑68 (MQ=255)
                                                        aaTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:1408565/68‑1 (MQ=255)
                                                        aaTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:1616738/68‑1 (MQ=255)
                                                        aaTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:88219/68‑1 (MQ=255)
                                                        aaTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:3224929/68‑1 (MQ=255)
                                                        aaTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:3152657/68‑1 (MQ=255)
                                                        aaTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:2687093/68‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:2799642/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:1999735/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:702186/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:967987/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:3023558/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:1649949/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:309572/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:1521609/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:2732355/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:1728876/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:1732874/46‑1 (MQ=255)
                                                        aaTTACAGACCCTTGATATTTTCTGCTTCTAATTCATT‑AAATATc                                    <  1:2276182/45‑1 (MQ=38)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:2017332/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:2353105/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:397730/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:1438326/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:307033/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:2959540/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:1327725/67‑1 (MQ=255)
                                                         aTTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:92633/67‑1 (MQ=255)
                                                          ttACAGACCCTAGATATTTTCTGCTTCTAATTCATTGAAATATc                                    <  1:62282/44‑1 (MQ=38)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:1774494/65‑1 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:2379066/65‑1 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:3223253/65‑1 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:1874488/65‑1 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtg          >  1:1157010/1‑69 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtg          >  1:621553/1‑69 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtg          >  1:388560/1‑69 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtg          >  1:1791347/1‑69 (MQ=255)
                                                           tACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtg          >  1:2774012/1‑69 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAg                 >  1:2020978/1‑61 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtgg         >  1:677947/1‑69 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtgg         >  1:1796093/1‑69 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtgg         >  1:1803097/1‑69 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtgg         >  1:2361293/1‑69 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtgg         >  1:979325/1‑69 (MQ=255)
                                                            aCAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCAtgg         >  1:2290636/1‑69 (MQ=255)
                                                                 ccTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTc              <  1:700173/59‑1 (MQ=255)
                                                                  cTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCa            <  1:877533/60‑1 (MQ=255)
                                                                  cTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCa            <  1:2826956/60‑1 (MQ=255)
                                                                   tttGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCATGGTGGAAgg  <  1:585050/69‑1 (MQ=255)
                                                                   tttGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCATGGTGGAAgg  <  1:1491356/69‑1 (MQ=255)
                                                                   |                                                                    
CTGACCCCCGATTTTAAAAAATATTGCCCTGAGCAAGGAGCCAGGGCAGGGATAACAATTACAGACCTTTGATATTTTCTGCTTCTAATTCATTGAAATATCTTAAAGTCTTAACTTTCAGCTCCATGGTGGAAGG  >  minE/426054‑426189

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