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
A1 F21 I0 R2 308 27.9 1975068 96.7% 1909890 67.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,918,430 G→A 33.3% L264L (CTG→TTG)  insK ← IS150 conserved protein InsB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,918,4300GA33.3% 103.4 / 74.9 81L264L (CTG→TTG) insKIS150 conserved protein InsB
Reads supporting (aligned to +/- strand):  ref base G (35/19);  new base A (18/9);  total (53/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCT  >  W3110S.gb/3918363‑3918490
                                                                   |                                                            
gACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCt                                                           <  1:1446304/71‑1 (MQ=255)
gACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCt                                                           <  1:1284954/71‑1 (MQ=255)
gACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCt                                                           <  1:64983/71‑1 (MQ=255)
gACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGGCAGACCTTTTAATTTCAAGCt                                                           <  1:1875408/71‑1 (MQ=255)
 aCAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCt                                                           <  1:1227774/70‑1 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:326330/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:237715/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:219181/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1956523/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1759816/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:330344/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1591715/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:416041/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1516923/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1457798/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:289767/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:309182/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1279092/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1191442/1‑71 (MQ=255)
      tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:860767/1‑71 (MQ=255)
       aaaCACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAttct                                                     >  1:1904827/1‑70 (MQ=255)
       aaaCACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAAttctt                                                    >  1:1661430/1‑71 (MQ=255)
       aaaCACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAAttctt                                                    >  1:1186979/1‑71 (MQ=255)
               ggCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCtgtt                                            <  1:1551958/71‑1 (MQ=255)
                gCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCtgtt                                            <  1:1582120/70‑1 (MQ=255)
                gCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCtgtt                                            <  1:267107/70‑1 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTctgctg                                              >  1:1070770/1‑63 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:1470982/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:217305/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:889502/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:1823480/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:527672/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:1586700/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagta                                      >  1:1376484/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtagca                                      >  1:41491/1‑69 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAAtt                                                       >  1:589707/1‑54 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:494530/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:1658222/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:1173263/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:116676/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:301201/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:597517/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:201158/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtagta                                      >  1:444818/1‑71 (MQ=255)
                     taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAACCTAATTCTTCTGCTGTTgtagta                                      >  1:464874/1‑71 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:450687/68‑1 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:99519/68‑1 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:672530/68‑1 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:736439/68‑1 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:976701/68‑1 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:990819/68‑1 (MQ=255)
                           tGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTc                                   <  1:1196979/68‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:1422917/70‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:1014993/70‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:1129965/70‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               >  1:94864/1‑70 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:1263974/70‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               >  1:1703362/1‑70 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               >  1:1424629/1‑70 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               >  1:1456185/1‑70 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:480264/70‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               >  1:402494/1‑70 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:1626874/70‑1 (MQ=255)
                             aTTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:1564499/70‑1 (MQ=255)
                               tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAatatat                            >  1:1143855/1‑71 (MQ=255)
                               tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAatatat                            >  1:1555788/1‑71 (MQ=255)
                                         aaTTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAg                  <  1:1460376/71‑1 (MQ=255)
                                           ttGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:520305/1‑71 (MQ=255)
                                           ttGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:1303462/1‑71 (MQ=255)
                                           ttGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:550055/1‑71 (MQ=255)
                                           ttGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:1435868/1‑71 (MQ=255)
                                                   aGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAg        >  1:1413987/1‑71 (MQ=255)
                                                   aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAg        >  1:42004/1‑71 (MQ=255)
                                                   aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAg        >  1:1494792/1‑71 (MQ=255)
                                                   aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAg        >  1:964162/1‑71 (MQ=255)
                                                   aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAg        >  1:1027748/1‑71 (MQ=255)
                                                    gACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGt                       <  1:943412/55‑1 (MQ=255)
                                                    gACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGt                       <  1:944383/55‑1 (MQ=255)
                                                    gACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCAGt                       <  1:52144/55‑1 (MQ=255)
                                                          ttAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCt  <  1:858702/70‑1 (MQ=255)
                                                             aTTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCt  <  1:981366/67‑1 (MQ=255)
                                                                   |                                                            
GACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCT  >  W3110S.gb/3918363‑3918490

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