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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,027,859 A→G 51.7% L232L (TTG→CTG)  yhhT ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,027,8590AG51.7% 6.5 / 85.6 60L232L (TTG→CTG) yhhTpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (9/20);  new base G (15/16);  total (24/36)
Fisher's exact test for biased strand distribution p-value = 1.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.69e-01

AACAGCAGCACCTGAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGACGAT  >  W3110S.gb/4027789‑4027925
                                                                      |                                                                  
aaCAGCAGCACCTGAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCaa                                                                    <  1:69060/71‑1 (MQ=255)
 aCAGCAGCACCTGAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCaaa                                                                   <  1:3469835/71‑1 (MQ=255)
   agcagcACCTGAATCATTGGCGGTACGGCGGAAATAACCGCGCCGATATTGGGCACGTAGTTGAGCaaa                                                                   <  1:3881294/69‑1 (MQ=255)
         aCCTGAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAg                                                           <  1:3268840/71‑1 (MQ=255)
            tGAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTAc                                                        >  1:1222334/1‑71 (MQ=255)
             gAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTAc                                                        >  1:4854627/1‑70 (MQ=255)
              aaTCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTAc                                                        >  1:2857977/1‑69 (MQ=255)
              aaTCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTAc                                                        >  1:3918706/1‑69 (MQ=255)
              aaTCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTAc                                                        >  1:4013605/1‑69 (MQ=255)
              aaTCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTg                                                      >  1:160493/1‑71 (MQ=255)
               aTCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGc                                                     >  1:5072886/1‑71 (MQ=255)
               aTCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGc                                                     >  1:1295605/1‑71 (MQ=255)
                tCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGcc                                                    <  1:334807/71‑1 (MQ=255)
                  aTTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCagaaa                                                                 >  1:2753381/1‑56 (MQ=255)
                  aTTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGGTGAGCAGAAACGCCAGTACTGccc                                                   <  1:1339628/70‑1 (MQ=255)
                   ttGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTAATGCCcac                                                 <  1:3914080/71‑1 (MQ=255)
                        ggTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTAc                                                        >  1:1344115/1‑59 (MQ=255)
                          tACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGc                                                              <  1:2393882/51‑1 (MQ=255)
                          tACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAgcg                                          >  1:719037/1‑71 (MQ=255)
                            gggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAg                                                           <  1:4559918/51‑1 (MQ=255)
                            cggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAg                                                           <  1:418119/52‑1 (MQ=255)
                            cggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAgcgc                                         <  1:4126840/70‑1 (MQ=255)
                            cggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCa                                        <  1:2698973/71‑1 (MQ=255)
                            cggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCa                                        <  1:1489241/71‑1 (MQ=255)
                             ggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCaa                                       <  1:4629231/71‑1 (MQ=255)
                             ggcggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCa                                        <  1:2319915/70‑1 (MQ=255)
                                ggAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAg                                                           <  1:3896078/48‑1 (MQ=255)
                                 gAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTg                                   >  1:966569/1‑71 (MQ=255)
                                 gAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTg                                   <  1:5103954/71‑1 (MQ=255)
                                  aaaTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGcc                                                             <  1:3361495/44‑1 (MQ=255)
                                  aaaTTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGc                                                              <  1:3771015/43‑1 (MQ=255)
                                   atttACCGCGCGGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTAc                                                        <  1:1843043/46‑1 (MQ=255)
                                   aaTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGcc                                                             <  1:1911249/43‑1 (MQ=255)
                                    aTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAg                                                           >  1:2748294/1‑44 (MQ=255)
                                    aTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAg                                                           >  1:887341/1‑44 (MQ=255)
                                    aTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAg                                                           >  1:757069/1‑44 (MQ=255)
                                    aTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACt                                                       >  1:4663505/1‑48 (MQ=255)
                                    aTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACAt                                               >  1:1868144/1‑56 (MQ=255)
                                    aTTACCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCAc                                <  1:882568/71‑1 (MQ=255)
                                       aCCGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCAcccc                             >  1:758770/1‑71 (MQ=255)
                                        ccGCGCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCAccccc                            <  1:1462644/71‑1 (MQ=255)
                                         cgcgCCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCAccccc                            <  1:2821623/70‑1 (MQ=255)
                                         cgcgCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAg                                                           <  1:3260992/39‑1 (MQ=255)
                                           cgcCGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGccc                                                   <  1:1758506/45‑1 (MQ=255)
                                           cgcCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTa                                                         >  1:2684442/1‑39 (MQ=255)
                                              cGATATTGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGc                      <  1:2090718/71‑1 (MQ=255)
                                               gATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCt                     <  1:1463047/71‑1 (MQ=255)
                                                atatTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCa                                 >  1:1887930/1‑58 (MQ=255)
                                                  atTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCa                                        <  1:4353924/49‑1 (MQ=255)
                                                   ttGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTg                                   <  1:1150644/53‑1 (MQ=255)
                                                   ttGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCTGCTcca                  <  1:8796/70‑1 (MQ=255)
                                                    tGGGCACGTAGTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTccagc                >  1:1225265/1‑71 (MQ=255)
                                                          cGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTccagccccagc          <  1:579109/71‑1 (MQ=255)
                                                           gTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTg                                   <  1:4183288/45‑1 (MQ=255)
                                                             aGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCa                                 >  1:1331213/1‑45 (MQ=255)
                                                              gTTGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGa      >  1:472091/1‑71 (MQ=255)
                                                              gTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCccagccag       <  1:174160/70‑1 (MQ=255)
                                                               ttGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCAcccc                             <  1:1204883/47‑1 (MQ=255)
                                                                tGAGCAGAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGAc     <  1:4276864/70‑1 (MQ=255)
                                                                tGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGAc     >  1:4135428/1‑70 (MQ=255)
                                                                  cgCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGc                                  <  1:2093218/38‑1 (MQ=255)
                                                                  aGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGACGAt  <  1:2954465/71‑1 (MQ=255)
                                                                    cAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGACGAt  <  1:4939183/69‑1 (MQ=255)
                                                                    cAAAAACGCCAGTACTGCCCACATCAGCGCAAACAGCAcccc                             >  1:2436164/1‑42 (MQ=255)
                                                                      |                                                                  
AACAGCAGCACCTGAATCATTGGCGGTACGGCGGAAATTACCGCGCCGATATTGGGCACGTAGTTGAGCAAAAACGCCAGTACTGCCCACATCAGCGCAAACTGCACCCCCATCAGCTCCAGCCCCAGCCAGACGAT  >  W3110S.gb/4027789‑4027925

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A