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 1,475,847 T→C 42.7% I304I (ATT→ATC)  nrdB → ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,475,8470TC42.7% 24.4 / 68.3 89I304I (ATT→ATC) nrdBribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like
Reads supporting (aligned to +/- strand):  ref base T (37/14);  new base C (23/15);  total (60/29)
Fisher's exact test for biased strand distribution p-value = 2.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

CAACAGGAGAAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCA  >  minE/1475779‑1475915
                                                                    |                                                                    
cAACAGGAGAAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACAtt                                                                      <  1:1904444/69‑1 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:2492153/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:957682/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:3426843/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:3042603/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:2860241/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:2409953/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:2332742/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:2066153/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:2017231/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:1530382/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:1461382/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGcc                                                               >  1:1303355/1‑68 (MQ=255)
        gaAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCCGAATAAAGACATTCTCTGcc                                                               >  1:1186594/1‑68 (MQ=255)
                   cGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGaa                                                    <  1:2174150/68‑1 (MQ=255)
                   cGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGaa                                                    <  1:3428180/68‑1 (MQ=255)
                   cGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGaa                                                    <  1:3222564/68‑1 (MQ=255)
                   cGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGaa                                                    <  1:1536313/68‑1 (MQ=255)
                   cGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGaa                                                    <  1:2781323/68‑1 (MQ=255)
                   cGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGaa                                                    <  1:2670709/68‑1 (MQ=255)
                    tgATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATa                                                  <  1:343183/68‑1 (MQ=255)
                    ggATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATa                                                  <  1:3187083/69‑1 (MQ=255)
                    ggATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATa                                                  <  1:3135101/69‑1 (MQ=255)
                    ggATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATa                                                  <  1:2633919/69‑1 (MQ=255)
                    ggATTATCTGTTCCGCGACGGTTCGATGATTGGGCTGAATAAAGACATTCTCTGCCAGTACGTTGAATa                                                  <  1:2234381/69‑1 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACg                                                         >  1:273982/1‑59 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACAt                                               >  1:3133081/1‑69 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACAt                                               >  1:1049193/1‑69 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACAt                                               >  1:2886230/1‑69 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACAt                                               >  1:1456852/1‑69 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACAt                                               >  1:84037/1‑69 (MQ=255)
                       ttATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTATCTGCCAGTACGTTGAATACAt                                               >  1:1340160/1‑69 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:179388/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:2988126/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:3004880/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:2744610/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:740642/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:74737/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:1575544/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:1793799/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:807894/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:1474872/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:1842255/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:2043673/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:3270247/69‑1 (MQ=255)
                                ccGTGATGGTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:3254579/69‑1 (MQ=255)
                                     aCGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTa                                 <  1:30951/69‑1 (MQ=255)
                                     aCGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTa                                 <  1:112820/69‑1 (MQ=255)
                                      tggTTCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatat                                      <  1:947035/62‑1 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:78234/1‑68 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:1629239/1‑68 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAatatg                                     >  1:2141156/1‑59 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:724350/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:3101011/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:498485/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1431136/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:3092019/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:608056/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:516775/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:343112/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1192522/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1933824/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1275600/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1259239/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:2143846/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1285624/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:826704/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:2332090/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:660279/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:2551775/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1781240/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:1735170/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:117580/1‑62 (MQ=255)
                                          tCGATGATTGGTCTGAATAAAGACATCCTCTGCCAGTACGTTGAATACATCACCAATATCCg                                   >  1:2910162/1‑62 (MQ=255)
                                           cGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgcagg                           <  1:178452/69‑1 (MQ=255)
                                             atgatTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgcaggca                         >  1:316579/1‑69 (MQ=255)
                                                      cTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAat                                        >  1:1112614/1‑45 (MQ=255)
                                                      cTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAat                                        >  1:3335679/1‑45 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:1997924/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:876803/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:227317/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:2367571/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:2731578/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:173984/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:674607/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:2951261/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:643735/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:1148506/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:54455/1‑49 (MQ=255)
                                                             aaGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATgca                             >  1:1504305/1‑49 (MQ=255)
                                                                    tctcTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCa  <  1:2710666/69‑1 (MQ=255)
                                                                    tctcTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCa  <  1:2422212/69‑1 (MQ=255)
                                                                    tctcTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCa  <  1:132633/69‑1 (MQ=255)
                                                                    tctcTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCa  <  1:1473337/69‑1 (MQ=255)
                                                                    tctcTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCa  <  1:2210970/69‑1 (MQ=255)
                                                                    tctcTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCa  <  1:1322298/69‑1 (MQ=255)
                                                                    |                                                                    
CAACAGGAGAAAGACTGGGCGGATTATCTGTTCCGCGACGGTTCGATGATTGGTCTGAATAAAGACATTCTCTGCCAGTACGTTGAATACATCACCAATATCCGTATGCAGGCAGTCGGTTTGGATCTGCCGTTCCA  >  minE/1475779‑1475915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A