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 2,340,553 C→A 30.2% intergenic (‑347/‑26) bipA ← / → glnA GTP‑binding protein/glutamine synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,340,5530CA30.2% 167.7 / 71.2 122intergenic (‑347/‑26)bipA/glnAGTP‑binding protein/glutamine synthetase
Reads supporting (aligned to +/- strand):  ref base C (41/44);  new base A (28/9);  total (69/53)
Fisher's exact test for biased strand distribution p-value = 5.56e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.48e-01

Only 100 of 126 total aligned reads displayed.

GATTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGATGCTGAACGAGCACGAA  >  minE/2340487‑2340620
                                                                  |                                                                   
gATTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCAt                                                                   <  1:517710/69‑1 (MQ=255)
gATTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCAt                                                                   <  1:1071769/69‑1 (MQ=255)
gATTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCAt                                                                   <  1:1801486/69‑1 (MQ=255)
gATTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCAt                                                                   <  1:3337310/69‑1 (MQ=255)
 aTTTCGCTTTATCTTTTTTACGGCGACACGGCCCATTTAATTGCAGATTTCGTTACCACGACGACAATg                                                                  <  1:1173660/69‑1 (MQ=255)
 aTTTCGCTTTATCTTTTTTACGGCGACACGGCCCATTTAATTGCAGATTTCGTTACCACGACGACAATg                                                                  <  1:1380177/69‑1 (MQ=255)
 aTTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCAt                                                                   <  1:1877903/68‑1 (MQ=255)
  tttCGCTTTATCTTTTTTACGGCGACACGGCCCATTTAATTGCAGATTTCTTTACCACGACGACAATg                                                                  <  1:138186/68‑1 (MQ=255)
  tttCGCTTTATCTTTTTTACGGCGACACGGCCCATTTAATTGCAGATTTCGTTACCACGACGACAATg                                                                  <  1:2402758/68‑1 (MQ=255)
  tttCGCTTTATCTTTTTTACGGCGACACGGCCCATTTAATTGCAGATTTCGTTACCACGACGACAATg                                                                  <  1:844916/68‑1 (MQ=255)
              ttttttACGGCGACACGGCCCATTTAATTGCAGATTTCGTTACCACGACGACAATg                                                                  <  1:2204347/56‑1 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:3117623/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:1708183/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:488289/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:3310152/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:1802936/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:2151810/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:2153028/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:2415737/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:2650008/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:772230/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:756023/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGgaga                                                    >  1:616499/1‑68 (MQ=255)
                ttttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACAAATCCAGgaga                                                    >  1:1176086/1‑68 (MQ=255)
                  ttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGt                                                  <  1:1692140/68‑1 (MQ=255)
                  ttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGt                                                  <  1:979767/68‑1 (MQ=255)
                  ttACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGt                                                  <  1:2927042/68‑1 (MQ=255)
                    aCGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTa                                                <  1:375481/68‑1 (MQ=255)
                    aCGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTa                                                <  1:2753327/68‑1 (MQ=255)
                    aCGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTa                                                <  1:1942649/68‑1 (MQ=255)
                    aCGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTa                                                <  1:2871711/68‑1 (MQ=255)
                     cGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTa                                                <  1:793094/67‑1 (MQ=255)
                       gCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:3413095/68‑1 (MQ=255)
                       gCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:3352824/68‑1 (MQ=255)
                       gCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:950291/68‑1 (MQ=255)
                       gCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:1473088/68‑1 (MQ=255)
                       gCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:225674/68‑1 (MQ=255)
                       gCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:1475405/68‑1 (MQ=255)
                               gCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCg                                     >  1:2851350/1‑68 (MQ=255)
                                ccAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGc                                    >  1:1050311/1‑68 (MQ=255)
                                 cAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTg                                  <  1:1482024/69‑1 (MQ=255)
                                 cAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTg                                  <  1:2758957/69‑1 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2977537/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:301170/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2834489/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:93770/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:900511/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2807957/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:3089114/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:58602/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2643876/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1926043/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1121177/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1211367/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1901530/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2543417/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2400948/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1737118/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2315663/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1309979/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:1360557/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGgag                                                     >  1:2237942/2‑46 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACCAATCCAGga                                                      >  1:778046/2‑45 (MQ=255)
                                     ttaatTGCAGATTTCGTTACCACGACGACAATGACAAATCCAGgag                                                     >  1:1267955/2‑46 (MQ=255)
                                     ataatTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAaca                              >  1:2391160/1‑69 (MQ=255)
                                     ataatTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAaca                              <  1:1018226/69‑1 (MQ=255)
                                       aatTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACg                            <  1:487385/69‑1 (MQ=255)
                                       aatTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACg                            <  1:803441/69‑1 (MQ=255)
                                        atTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTa                                           <  1:510749/53‑1 (MQ=255)
                                        atTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTa                                           <  1:2674958/53‑1 (MQ=255)
                                        atTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTa                                           <  1:3176680/53‑1 (MQ=255)
                                          tGCAGATTTCGTTATCACGACGACCATGACCAATCCAGGAGAGTTaaat                                             <  1:592100/49‑2 (MQ=255)
                                          tGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTa                          <  1:324262/68‑1 (MQ=255)
                                          tGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTa                          <  1:3132625/68‑1 (MQ=255)
                                          tGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTa                          <  1:2844827/68‑1 (MQ=255)
                                          tGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTa                          <  1:1447096/68‑1 (MQ=255)
                                              gATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGAc                     <  1:1805039/69‑1 (MQ=255)
                                                 ttCGTTCCCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGa                   >  1:436841/1‑68 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGa                   >  1:1017698/1‑68 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGa                   >  1:1193396/1‑68 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:1354182/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:3257101/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:3275865/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:259301/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:1222841/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:2588934/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:2774246/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:345221/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:745050/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:677480/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:231509/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:1891656/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:1883469/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:1656550/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:2167461/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGAt                  >  1:194990/1‑69 (MQ=255)
                                                 ttCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACGGACGAt                  >  1:3344784/1‑69 (MQ=255)
                                                        ccACGACGACCATGACCAATCCAGGAGAGTTAAAg                                             <  1:2103171/35‑1 (MQ=255)
                                                                  cATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGATGCTGAACGAGCACgaa  >  1:2899222/1‑68 (MQ=255)
                                                                  cATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGATGCTGAACGAGCACgaa  >  1:2686807/1‑68 (MQ=255)
                                                                  |                                                                   
GATTTCGCTTTATCTTTTTTACGGCGACACGGCCAAAATAATTGCAGATTTCGTTACCACGACGACCATGACCAATCCAGGAGAGTTAAAGTATGTCCGCTGAACACGTACTGACGATGCTGAACGAGCACGAA  >  minE/2340487‑2340620

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