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 401,428 A→G 24.6% T36T (ACT→ACC)  dacA ← D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE401,4280AG24.6% 100.7 / 29.4 85T36T (ACT→ACC) dacAD‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base A (30/34);  new base G (12/9);  total (42/43)
Fisher's exact test for biased strand distribution p-value = 4.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGAGTTATAGTCAATCAGGATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCGTGGTG  >  minE/401366‑401491
                                                              |                                                               
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:2872013/68‑1 (MQ=255)
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:2976528/68‑1 (MQ=255)
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:773939/68‑1 (MQ=255)
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:3086921/68‑1 (MQ=255)
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:1257569/68‑1 (MQ=255)
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:1930588/68‑1 (MQ=255)
ccGGAGTTGTAGTCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:3398054/68‑1 (MQ=255)
ccGGAGTTATAGTCAATCAGGATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGtttt                                                            <  1:3183972/68‑1 (MQ=255)
ccGGAGTTATAGTCAATCAGGATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGtttt                                                            <  1:2267754/68‑1 (MQ=255)
            tCAATCAGGATGTAGGACTCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:2222969/56‑1 (MQ=255)
             cAATCAGGATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCAt                                              >  1:681262/1‑69 (MQ=255)
             cAATCAGGATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCAt                                              >  1:1097863/1‑69 (MQ=255)
                    gATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCTtg                                       <  1:1486241/69‑1 (MQ=255)
                    gATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       <  1:1934851/69‑1 (MQ=255)
                    gATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       <  1:1889922/69‑1 (MQ=255)
                    gATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       <  1:1996447/69‑1 (MQ=255)
                    gATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       <  1:1801745/69‑1 (MQ=255)
                    gATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       <  1:2610337/69‑1 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:2547085/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:262790/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:2528988/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:3034184/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:368304/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:427020/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:479133/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:999335/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       <  1:2210117/68‑1 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:1047947/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:1488941/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:126329/1‑68 (MQ=255)
                     aTGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCAtg                                       >  1:1726294/1‑68 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          >  1:1987735/1‑46 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          <  1:3189211/46‑1 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          <  1:3299850/46‑1 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          <  1:369675/46‑1 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          >  1:1192388/1‑46 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          >  1:1778975/1‑46 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          >  1:1853804/1‑46 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          <  1:2518791/46‑1 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          <  1:1164693/46‑1 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          <  1:839402/46‑1 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          >  1:1945713/1‑46 (MQ=255)
                        tAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGa                                                          >  1:2049087/1‑46 (MQ=255)
                             cTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGat                                                         >  1:325231/1‑42 (MQ=255)
                             cTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgcag                                  >  1:359702/1‑65 (MQ=255)
                             cTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCaga                              <  1:1017080/69‑1 (MQ=255)
                             cTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCaga                              <  1:1536855/69‑1 (MQ=255)
                             cTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCaga                              <  1:9134/69‑1 (MQ=255)
                             cTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCaga                              <  1:1415038/69‑1 (MQ=255)
                              tCCGCGTCGATCTGCGGTACACCCGGGATCATGGtttt                                                            <  1:491049/38‑1 (MQ=38)
                                cGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAgaga                            >  1:1930725/1‑68 (MQ=255)
                                cGCATCGATCTGCGGTAAACCCGGGATCATATTTTTGATATTCAGGTCATCGGCAtg                                       <  1:2636636/57‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:2185856/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:1415819/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:297265/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:1336651/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:240817/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:1952906/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:2222237/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:750955/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:2547161/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:2227682/54‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGc                     <  1:1996980/69‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGc                     >  1:3127346/1‑69 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGc                     <  1:2179228/69‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGc                     <  1:2306253/69‑1 (MQ=255)
                                      gATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGc                     >  1:2648296/1‑69 (MQ=255)
                                       aTCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTgc                                    <  1:891409/53‑1 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:508060/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:2169818/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:873289/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:694140/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:1469739/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:2668586/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:1577574/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:2892526/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:2973005/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:3420125/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATaa                         >  1:3174923/1‑46 (MQ=255)
                                                         aTCATGGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATa                          >  1:2411842/1‑45 (MQ=255)
                                                         aTCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCgtggtg  >  1:2753524/1‑69 (MQ=255)
                                                         aTCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCgtggtg  >  1:1771344/1‑69 (MQ=255)
                                                         aTCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCgtggtg  >  1:2920040/1‑69 (MQ=255)
                                                         aTCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCgtggtg  >  1:860886/1‑69 (MQ=255)
                                                         aTCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCgtggtg  >  1:1537052/1‑69 (MQ=255)
                                                              |                                                               
CCGGAGTTATAGTCAATCAGGATGTAGGACTCCGCATCGATCTGCGGTACACCCGGGATCATAGTTTTGATATTCAGGTCATCGGCATGTGCAGCAGAGATAAAGGCTGTGCAAAGAGCCGTGGTG  >  minE/401366‑401491

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