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 F8 I0 R2 422 46.8 3726540 94.7% 3529033 61.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,013,681 G→A 79.7% V11V (GTC→GTT)  yqeC ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,013,6810GA79.7% 133.4 / 31.9 64V11V (GTC→GTT) yqeCconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (3/10);  new base A (24/27);  total (27/37)
Fisher's exact test for biased strand distribution p-value = 2.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

AGCTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATAAA  >  W3110S.gb/3013614‑3013740
                                                                   |                                                           
agcTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACt                                                          <  1:1670619/71‑1 (MQ=255)
agcTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:3347702/71‑1 (MQ=255)
      ttttCCCCCCAGCACCAACAACAGAAATCACATTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGcc                                                    <  1:3701193/71‑1 (MQ=255)
      ttttCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGcc                                                    <  1:3445921/71‑1 (MQ=255)
       tttCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGcc                                                    >  1:1001011/1‑70 (MQ=255)
        ttCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGa                                                  >  1:3149557/1‑71 (MQ=255)
                  cACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAAc                                         >  1:3068398/1‑70 (MQ=255)
                  cACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAAc                                         >  1:1077334/1‑70 (MQ=255)
                  cACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGACGATGGGTCAAc                                         >  1:1513562/1‑70 (MQ=255)
                   aCCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACta                                       >  1:3493749/1‑71 (MQ=255)
                   aCCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACta                                       >  1:908580/1‑71 (MQ=255)
                     caacaaCAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtata                                     >  1:1485062/1‑71 (MQ=255)
                     caacaaCAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtata                                     >  1:2818657/1‑71 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:1264673/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:1377825/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:1387277/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:694116/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:2585821/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:253503/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:3673428/38‑1 (MQ=255)
                                 tCACAGTGGGACGTTTCTGCGCACCT‑AATCAATAACt                                                          <  1:836670/37‑1 (MQ=37)
                                 tCACAGTGGGACGTTGCTGCGCACCTAAATCATTAACt                                                          <  1:2542851/38‑1 (MQ=25)
                                    caGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:93728/71‑1 (MQ=255)
                                    caGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2602599/71‑1 (MQ=255)
                                    caGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:3685299/71‑1 (MQ=255)
                                    caGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:483089/71‑1 (MQ=255)
                                    caGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2933118/71‑1 (MQ=255)
                                    caGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:3307830/71‑1 (MQ=255)
                                     aGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:1445760/70‑1 (MQ=255)
                                         ggACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATg                  <  1:3239709/70‑1 (MQ=255)
                                         ggACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATg                  <  1:2002977/70‑1 (MQ=255)
                                              tttCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2175643/61‑1 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtata                                     >  1:456449/1‑44 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:3223793/1‑61 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:416349/1‑61 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctctct          >  1:264060/1‑71 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctctct          >  1:3514132/1‑71 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctctct          >  1:3002013/1‑71 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctctct          >  1:2007568/1‑71 (MQ=255)
                                                tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctctct          >  1:2427441/1‑71 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:997007/41‑1 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:447731/41‑1 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:623137/41‑1 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:76967/41‑1 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:3268935/41‑1 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:1154377/41‑1 (MQ=255)
                                                        ccTAAATCAATAACTAATGCCGATGGGTCAACTATACtttt                                <  1:2192375/41‑1 (MQ=255)
                                                          tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:1235992/1‑51 (MQ=255)
                                                          tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:1240573/1‑51 (MQ=255)
                                                            aaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:2444297/37‑1 (MQ=255)
                                                            aaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:1417541/37‑1 (MQ=255)
                                                            aaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:2156882/37‑1 (MQ=255)
                                                            aaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:1928753/37‑1 (MQ=255)
                                                            aaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:1776853/37‑1 (MQ=255)
                                                            aaTCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:1812760/47‑1 (MQ=255)
                                                            aaTCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2321220/47‑1 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACg                            >  1:3393307/1‑39 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:3696834/1‑47 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:673556/1‑47 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:1413737/1‑47 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:1198519/1‑47 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:3254358/1‑47 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTa                    >  1:1016584/1‑47 (MQ=255)
                                                              tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATaaa  >  1:3082473/1‑65 (MQ=255)
                                                                   |                                                           
AGCTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATAAA  >  W3110S.gb/3013614‑3013740

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